Thèse de doctorat : Sciences du vivant. Biologie cellulaire et moléculaire : Strasbourg : 2009. Thèse de doctorat : Sciences du vivant. Biologie cellulaire et moléculaire : Boston : 2009. / Thèse soutenue sur un ensemble de travaux. Thèse soutenue en co-tutelle. Titre provenant de l'écran-titre. Bibliogr. 11 p.

Thesis (Ph. D.)--West Virginia University, 2009. / Title from document title page. Document formatted into pages; contains ix, 89 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 82-88).

Thesis (Ph.D.) - University of Glasgow, 2007. / Ph.D. thesis submitted to the Division of Biochemistry and Molecular Biology, Biomedical and Life Sciences (IBLS), University of Glasgow, 2007. Includes bibliographical references. Print version also available.

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

In Arabidopsis thaliana, a gene family encodes acyl-CoA-binding proteins (ACBPs) conserved at the acyl-CoA-binding domain which facilitates the binding to acyl-CoA esters. These ACBPs, designated ACBP1 to ACBP6, range in size from 10.4 to 73.1 kD. Previous studies have shown that the the overexpression of ACBP1 or ACBP2 in Arabidopsis likely promotes repair of lipid membranes and result in enhanced tolerance to lead and cadmium, respectively. Microarray data (http://bar.utoronto.ca/) revealed that the expression of ACBP1 and ACBP2 is also regulated by other abiotic stresses, such as cold and drought, suggestive of their association with these environmental pressures. The aim of this study is to investigate and better understand the roles of ACBP1 and ACBP2 in different stress responses. It has been previously observed that the expression of both ACBP1 and ACBP4 is lead [Pb(II)]-inducible and recombinant ACBP1 and ACBP4 bind Pb(II) in vitro. In this study, ACBP1 and ACBP4 were overexpressed in Brassica juncea to test if these ACBPs could be extended for application in Pb(II) phytoremediation in transgenic B. juncea. On freezing (-12 to -8 °C) treatment, ACBP1-overexpressing Arabidopsis was freezing sensitive and accumulated more phosphatidic acid (PA), but less phosphatidylcholine (PC), in contrast to acbp1 mutant plants which were freezing tolerant and had reduced PA and elevated PC levels. Such changes in PC and PA were consistent with the expression of the mRNA encoding phospholipase D1 (PLD1), a major enzyme that promotes the hydrolysis of PC to PA. In contrast, the expression of phospholipase D (PLD), which plays a positive role in freezing tolerance, was up-regulated in acbp1 mutant plants and down-regulated in ACBP1-overexpressing plants. Reduced PLD1 expression and decreased hydrolysis of PC to PA may enhance membrane stability in the acbp1 mutant plants. Given that recombinant ACBP1 binds PA and acyl-CoA esters in vitro, the expression of PLD1 and PLD could be regulated by PA or acyl-CoAs maintained by ACBP1, if ACBP1 were to resemble the yeast 10-kD ACBP by its capability to modulate gene expression during stress responses. Interestingly, another membrane-associated ACBP, ACBP2, which shows high (76.9%) conservation in amino acid homology to ACBP1, did not appear to be affected by freezing treatment. Besides freezing stress, ACBP1, as well as ACBP2, have been observed to participate in abscisic acid (ABA) signaling. They both promote ABA signaling in seed germination and seedling development, while only ACBP2 is involved in the drought response. The overexpression of ACBP2 in Arabidopsis up-regulated reactive oxygen species (ROS) production culminating in reduction in stomatal aperture and water loss in guard cells, thereby enhancing drought tolerance. For tests in phytoremediation, B. juncea was selected for overexpression of ACBP1 and ACBP4 because it is fast-growing, has a higher biomass than Arabidopsis, and is known to be a good accumulator of Pb(II). However, results of Pb(II) treatment for two days showed that the overexpression of ACBP1 or ACBP4 in B. juncea did not significantly improve Pb(II) tolerance. Nevertheless, B. juncea overexpressing ACBP1 did accumulate Pb(II) in roots whereas ACBP4-overexpressing B. juncea lines accumulated Pb(II) in both shoots and roots. Given that B. juncea has a larger biomass than Arabidopsis, it is likely that the duration of Pb(II)-incubation tested in this study was not drastic enough for comparison, and the incubation time should be further extended for Pb(II) translocation. In addition, future studies on Arabidopsis should be conducted to better understand the mechanism of ACBP4-mediated Pb(II) accumulation using Arabidopsis acbp4 mutant and ACBP4-overexpressing plants. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

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Telomeres are the ends of linear chromosomes tasked with preventing their recognition by the DNA damage machinery and providing a mechanism to solve the end replication problem. The telomeric DNA is mostly double-stranded, but it terminates in a 3’ protrusion termed the G-overhang. Telomeres utilize telomerase, a reverse transcriptase, to elongate the telomere, and thus, solve the end replication problem. Both the double strand region and the G-overhang are bound by specific proteins to facilitate the objectives of the telomere. First discovered in budding yeast, the CST (Cdc13(CTC1)/Stn1/Ten1) complex binds to the G-overhang and is important for both chromosome end protection and telomere replication. Work reported in this dissertation provided the first evidence that CST was present outside of yeast, which led to its subsequent identification in a number of vertebrates. Here I present the identification and characterization of the three components of CST in Arabidopsis thaliana. Similar to yeast, Arabidopsis CST is required for telomere length maintenance, for preventing telomere recombination and chromosome end-to-end fusions. Mutations in the CST complex result in severe genomic instability and stem cells defects. My research also shows that CST and telomerase act synergistically to maintain telomere length. Together these data provide evidence for an essential role for CST in maintaining telomere integrity. Unexpectedly, I discovered that the TEN1 component of CST may have a more complex role than other members of the heterotrimer. The majority of telomere-related functions we can assay using molecular and cytological approaches are shared by CTC1, STN1 and TEN1, though TEN1 has additional roles in maintaining genome stability, modulating telomerase activity and possibly non-telomeric functions in the chloroplast. I also present genetic evidence that TEN1 and STN1 act in the same pathway for the maintenance of telomere length and chromosome end protection. Interestingly, however, disrupting the STN1/TEN1 interaction reveals a separation of STN1 function for chromosome end protection versus telomere length maintenance. Finally, I describe the design and creation of a library of STN1 and TEN1 mutants that will be used to further characterize their functions and their interaction partners. By disrupting such interactions, it will be possible to elucidate the functional significance of these interactions, and thus, provide new insight into how CST functions in Arabidopsis.

Photosynthetic eukaryots emerged as a result of several billion years of evolution between proeukaryotic cell and ancestral cyanobacteria that formed modern chloroplasts. The symbiotic relationship led to significant rearrangements in the genomes of the plastid and the nucleus: as many as 90 % of all the plastid genes were transferred to the nucleus. The gene transfer has been accompanied by the development of sophisticated regulatory signaling networks originating in the organelle (retrograde) and in the nucleus (anterograde) that coordinate development of the plastid and ensure adequate cell responses to stress signals. In this thesis I have demonstrated that transcriptional activity of PEP in the chloroplast is essential for proper embryo and seedling development in Arabidopsis thaliana. The function of PEP is dependent on the nuclear encoded PEPassociated factor PRIN2 that is able to sense the redox status of the plastid during seedling development and different stress. In response to the plastid status PRIN2 modulates the transcription activity of the PEP enzyme complex. We further established that PRIN2, as an essential component for full PEP activity, is also required to emit the Plastid Gene Expression (PGE) retrograde signal to regulate the Photosynthesis-Associated Nuclear Genes (PhANG) in the nucleus during early seedling growth via GUN1. On the other hand, regulation of PhANG expression during the High Light (HL) conditions requires functional PRIN2 and PEP activity but is GUN1-independent. Another retrograde signal produced by the developing chloroplast is associated with the tetrapyrrole biosynthesis pathway. We have established that accumulation of the chlorophyll intermediate MgProtoIX-ME in the crd mutant triggers repression of the PhANG expression, and this negative signal is mediated by a cytoplasmic protein complex containing the PAPP5 phosphatase. The nuclear targets that receive the tetrapyrrole mediated signal are GLK1 and GLK2 transcription factors that control the PhANG expression and the expression of the enzymes involved in the biosynthesis of chlorophyll. / Fotosyntetiserande eukaryoter uppstod från en endosymbiotisk interaktion under några miljarder år mellan en ur-eukaryot och kloroplastens förfader, den prokaryota cyanobakterien. Den symbiotiska händelsen ledde till att kloroplastens och kärnans genom blev väsentligt förändrade. Så småningom överförde kloroplasten så många som 90 % av dess gener till cellkärnan. För att koordinera genutrycket från de två genomen utvecklade växtcellen ett sofistikerat signalsystemen som inkluderar: plastid-kärn (retrograd) och kärn-plastid (anterograd) signalering som styr kloroplastens utveckling och förmåga att anpassa sig till stressförhållanden. Den här avhandlingen beskriver kloroplastens maskineri för genuttryck (PEP) som en nödvändig komponent för embryo- och växtutvecklingen hos Arabidopsis thaliana. PEP funktionen är beroende av det kärnkodade kloroplastproteinet PRIN2 som är associerat med PEP. PRIN2 mottar redox signaler från plastiden och förändrar genuttrycksaktivitet under kloroplastens utvecklingen eller under olika stressförhållanden. Jag visar dessutom att PRIN2 spelar en viktig roll i överföring av kloroplastens signal som kommunicerar genuttrycksaktivitet (PGE) via GUN1 till kärnan där den styr uttryck av de kärnkodade fotosyntetesgenerna (PhANG). Under högljus stressförhållanden styrs dock PhANG-uttrycket av signaler som uppstår från PEP-aktivitet och PRIN2 men som är oberoende av GUN1. Vidare finns det en annan retrograd signal som har sitt ursprung i biosyntesen av tetrapyrroler. Jag har visat att ackumuleringen av tetrapyrrolen MgProtoIX-ME i crd-mutanten framkallar nedreglering av PhANG-uttryck genom interaktion med ett fosfatas (PAPP5) i cytosolen. GLK1 and GLK2 är två transkriptionsfaktorer som tar emot den tetrapyrrole-medierade signalen i sin tur styr biosyntes av chlorofyll och PhANG uttryck.

Programmed Cell Death (PCD) describes an orderly cellular breakdown that occurs in both plants and animals throughout development and in response to biotic and abiotic stresses. The molecular machinery that functions in the induction and execution of animal PCD has been characterised in great detail. Conversely, few genes and proteins involved in plant PCD have been identified. While certain features of animal PCD may be conserved, the induction and execution of plant PCD is also likely to involve novel proteins and mechanisms. The aim of the work presented in this thesis was to investigate experimental approaches for studying plant PCD and to gain an understanding of the molecular mechanisms involved. To this end, an Arabidopsis thaliana cell suspension system was developed in which PCD could be induced by both a heat treatment (55°C, 10 min) and senescence (13 to 14 days-old). This system allowed for the molecular responses related to programmed cell death to be distinguished from those that were a specific response to the inducing stimulus. The Arabidopsis cell suspension system was utilised for an analysis of transcriptomic and proteomic changes that occur following the induction of PCD. A custom cDNA microarray analysis of ~100 putative cell death-related genes was used to measure the abundance of transcripts of these genes during PCD, and this work was extended to a whole-genome transcriptomic analysis of PCD. A number of candidate genes that may play a role in plant PCD were identified. These included those encoding antioxidant enzymes, cytosolic heat shock proteins, the mitochondrial adenine nucleotide translocase, ion transporters, a two-component response regulator (ARR4), several pathogenesis-related proteins, phospholipases and proteases, extracellular glycoproteins and enzymes (including a subtilisin-like protease, chitinases, and glucanases), and transcriptional regulators such as a homeobox leucine zipper and NAC-domain proteins. The induction and execution of plant PCD is also likely to involve mechanisms that are not transcriptionally regulated. A proteomic analysis of changes in the total cellular protein profile during heat- and senescence-induced PCD was therefore used to identify 12 proteins that are modulated in both systems and may play a PCD-specific role. These included the mitochondrial voltage-dependent anion channel (Athsr2), catalase, mitochondrial superoxide dismutase, an extracellular glycoprotein, and aconitase. Selected genes and proteins identified in the transcriptomic and proteomic analyses were further investigated in an attempt to define their role in plant PCD. Since PCD is difficult to quantitatively analyse at the whole-plant level, initially a strategy of transient expression of genes of interest in Arabidopsis protoplasts was adopted. However, it proved to be technically difficult to accurately quantify the number of dead cells in this system. As an alternative, Arabidopsis T-DNA insertional mutants within genes of interest were investigated for PCD-related phenotypes. Mutants in Senescence-Related Gene 3, the mitochondrial voltage-dependent anion channel (Athsr2), and cytosolic Heat shock protein 70-3 were isolated. The mutant lines were not visibly affected in their development, formation of xylem, onset and progression of senescence, or responses to abiotic and biotic stresses. This indicated that these genes are either not involved in the PCD pathway or that their functional role can be fulfilled by other gene products.